Ofcourse I spoke too soon…
I get a problem in that the conversion of my dataset reports that it cannot find the chromosome length files, even though trickster itself has no problem showing it…
I looked at the problem script and it is showing below
It seems that the script is passed the path to the chromosome files like this “tool-data/shared/ucsc/chrom/hg19-decoy.len”
This will clearly never work since this file is not relative to the working directory..
SO somewhere a script forgets to add the ${GALAXY_DATA_DIR} or whatever that parameter is…..
I could probably hardcode the location of the tool-data directory, but I don’t think that should be the solution…
Why do I only have this issue? SHOULD I have hardcoded the location of tool-data?
The universe_wgi.ini.sample file does not hardcode this…
Am I missing some updates?
Thanks,
Thon
#!/bin/sh
GALAXY_LIB="None"
if [ "$GALAXY_LIB" != "None" ]; then
if [ -n "$PYTHONPATH" ]; then
PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
else
PYTHONPATH="$GALAXY_LIB"
fi
export PYTHONPATH
fi
TMPDIR=/mnt/ngs/analysis/svcgalaxy/DATATEST/TMP
export TMPDIR
cd /mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916
grep -v '^#' /mnt/ngs/analysis/svcgalaxy/DATATEST/files/002/dataset_2288.dat | sort -k1,1 | bedtools genomecov -bg -split -i stdin -gtool-data/shared/ucsc/chrom/hg19-decoy.len > temp.bg ; bedGraphToBigWig temp.bg tool-data/shared/ucsc/chrom/hg19-decoy.len/mnt/ngs/analysis/svcgalaxy/DATATEST/files/002/dataset_2315.dat; cd /mnt/ngs/analysis/svcgalaxy/galaxy-test; /mnt/ngs/analysis/svcgalaxy/galaxy-test/set_metadata.sh /mnt/ngs/analysis/svcgalaxy/DATATEST/files /mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916 . /mnt/ngs/analysis/svcgalaxy/galaxy-test/universe_wsgi.ini /mnt/ngs/analysis/svcgalaxy/DATA/TMP/tmp2KAn7W /mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/galaxy.json /mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/metadata_in_HistoryDatasetAssociation_2551_XsCZer,/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/metadata_kwds_HistoryDatasetAssociation_2551_iNUAr_,/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/metadata_out_HistoryDatasetAssociation_2551_ZHhosg,/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/metadata_results_HistoryDatasetAssociation_2551_tqtiIX,,/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/metadata_override_HistoryDatasetAssociation_2551_MOfd8w
echo $? > /mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/galaxy_1916.ec
Regards,
Thon
Thon deBoer Ph.D., Bioinformatics Guru
California, USA |p: +1 (650) 799-6839 |m: thondeboer@me.com
From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Thon de Boer
Sent: Friday, August 23, 2013 5:47 PM
To: 'Jeremy Goecks'
Cc: 'Galaxy-dev Galaxy-dev'
Subject: Re: [galaxy-dev] Why does my trackster complain about not being able to display BED files?
I tracked it down to a problem with the API proxy configuration.
I had the API calls diverted to a different server since I wanted to ensure that API calls would be handled by a different server, but that does not seem to work correctly for the API calls used in trickster…
Issue resolved…
Regards,
Thon
Thon deBoer Ph.D., Bioinformatics Guru
California, USA |p: +1 (650) 799-6839 |m: thondeboer@me.com
I now have a different problem with a different (production) version of galaxy trickster.
I always get this message “Could not load chroms for this dbkey”
I have checked that I have files with the [key].len in tool-data/shared/ucsc/chrom and I have twobit files etc.
The weird thing is, that the “Create visualization” shows the genome keys I have but this window shows nothing for the dbkey it things it should be getting…
So somewhere it “looses” the key…
Any ideas?
(I’m running the latest update)
<image001.png>
Regards,
Thon
Thon deBoer Ph.D., Bioinformatics Guru
California, USA |p: +1 (650) 799-6839 |m: thondeboer@me.com
Thanks Jeremy,
I did what you suggested and now it no longer complains!
Not sure if I had edited datatypes_conf.xml but just copying the sample worked and let’s just hope I did not break any of my changes
Regards,
Thon
Thon deBoer Ph.D., Bioinformatics Guru
California, USA |p: +1 (650) 799-6839 |m: thondeboer@me.com
From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu]
Sent: Thursday, August 22, 2013 11:11 AM
To: Anthonius deBoer
Cc: sam guerler; Galaxy-dev Galaxy-dev
Subject: Re: [galaxy-dev] Why does my trackster complain about not being able to display BED files?
Am I missing a converter?
Yes, you are missing the bed_to_bigwig converter.
If you haven't made changes to your datatypes_conf.xml file, you can just copy datatypes_conf.xml.sample to datatypes_conf.xml to get the needed converters.
If you've made changes to datatypes_conf.xml, you'll need to manually add the needed converters. We recently transitioned all the *_to_summary_tree converters to *_to_bigwig, so you'll want to remove the summary_tree converters and replace them with the bigwig converters.
And why would a BED file even needed to be converted?
Converter = indexer for visualizations. Datasets are indexed so that (a) aggregate (coverage) data is readily available when viewing a large region and (b) finding features in a small region (when zoomed in) is fast.